Protein WP_040659554.1 in Oscillibacter ruminantium GH1
Annotation: NCBI__GCF_000307265.1:WP_040659554.1
Length: 511 amino acids
Source: GCF_000307265.1 in NCBI
Candidate for 21 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
D-mannose catabolism | HSERO_RS03640 | lo | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 38% | 97% | 334.3 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
D-cellobiose catabolism | mglA | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
D-glucose catabolism | mglA | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
lactose catabolism | mglA | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
D-maltose catabolism | mglA | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
sucrose catabolism | mglA | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
trehalose catabolism | mglA | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
D-xylose catabolism | xylG | lo | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 39% | 99% | 333.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
myo-inositol catabolism | PS417_11890 | lo | m-Inositol ABC transporter, ATPase component (itaA) (characterized) | 38% | 94% | 328.6 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
D-fructose catabolism | frcA | lo | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 38% | 96% | 315.8 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
sucrose catabolism | frcA | lo | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 38% | 96% | 315.8 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-fucose catabolism | BPHYT_RS34245 | lo | ABC transporter related; Flags: Precursor (characterized, see rationale) | 33% | 98% | 270 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-rhamnose catabolism | BPHYT_RS34245 | lo | ABC transporter related; Flags: Precursor (characterized, see rationale) | 33% | 98% | 270 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-alanine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-leucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-proline catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-serine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-threonine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 87% | 111.7 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 30% | 91% | 107.5 | Autoinducer 2 import ATP-binding protein LsrA; AI-2 import ATP-binding protein LsrA; EC 7.6.2.- | 43% | 387.1 |
Sequence Analysis Tools
View WP_040659554.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
Sequence
MSTEQASTSAGQLLSVQNIRKSFGLNAVLKGISLDVAPGEILALVGGNGAGKSTLMKIIM
GIYTQDGGDIYIKGEHVVLNKPAQALAKGIYMVPQEPLLFPNMTVEENITIGFSQNKAEL
HRELVATMDEIGWHLNLTRRASSLSIAEQQLVEILRGLLRHAQILILDEPTSALTFDEVE
SLFKCVRDLQSKGIGIIYITHRLTEVFELATHVAIMRDGIIAVKGAVSGFTREDLVRGLL
PPDMDACKDGGCPVPTAVDYTKAPVLELQNFGGYGFSGINLKIYPGEILGMAGVVGAGRT
ELATTIFGMDKVLGGKVLLNGRDITGLKTRAVIQAGLNYVPEDRHLNGLFKISDVACNTS
SALLGDGSLGKFLLNRKKEQTLTQRYVDDFRTKITGQEQAVGSLSGGNQQKVVIARSLST
SPRVIILDEPTRGIDAAARGDVYRIIHQLRDQGVSILLISSDMEEIVELADRAVTVFQGR
VNGEFKGADINQDRLMAAAFGVSEEKVASGS
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
About GapMind
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory